Chronic obstructive pulmonary disease (COPD) is a chronic debilitating disease that afflicts ~24 million Americans and is the fourth leading cause of death in the US and in the world. The lower airway microbiome of adults with COPD harbors bacterial pathogens that are absent in the lower airway microbiome of healthy people. In rigorous prospective studies, nontypeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat) are by far the most common bacterial pathogens that persist in the lower airways in COPD. The presence of these pathogens in the lower airways has profound consequences on the clinical course and pathogenesis of the disease. Persistent bacteria induce airway inflammation that results in increased symptoms, enormous morbidity, and also leads to acceleration of the progressive loss of lung function that leads to early mortality in COPD. Our work over the last five years has provided key observations to guide the work proposed here to advance the field by identifying mechanisms by which these exclusively human pathogens persist in the unique environment of COPD airways. For example, while NTHi and Mcat are classically considered to be extracellular pathogens, multiple lines of evidence now show that both pathogens invade and survive in human respiratory epithelial cells and macrophages, resulting in a reservoir of intracellular bacteria that resist clearance by antibiotics and host mechanisms. In aim 1, we will elucidate the evolutionary dynamics of bacterial pathogens in the natural environment of the human COPD airways by analyzing the genomes of serial isolates of strains of NTHi and Mcat that have persisted for months to years. In aim 2, we will examine transcriptional profiles of serial isolates of persistent strains and transcripts from fresh sputum samples collected from adults with COPD with persistent NTHi and Mcat to identify gene products that undergo changes that enable persistence in COPD airways. In Aim 3, guided by dynamic changes in genomes and transcriptomes in human airways, we will elucidate mechanisms that mediate persistence of NTHi and Mcat using relevant model systems. This work will lead directly to an innovative approach of identifying specific targets for intervention through pathogen-specific eradication and/or anti-virulence antimicrobial agents, which would leave the normal microbiota undisturbed. This approach has far-reaching clinical benefits, representing a completely novel approach to treating bacterial infection in COPD, which has relied on traditional antibiotics for 70 years.